The Swedish kings Eric XIV (1560–68) and Charles IX (1604–1611) took their numbers according to a fictitious History of Sweden. He was actually the third Swedish king called Charles.

He came into the throne by championing the Protestant cause during the increasingly tense times of religious strife between competing sects of Christianity. In just over a decade, these would break out as the Thirty Years' War. These conflicts had already caused the dynastic squabble rooted in religious freedom that deposed his nephew and brought him to rule as king of Sweden.

His reign marked the start of the final chapter (dated 1648 by some) of both the Reformation and Counter-reformation. With his brother's death in November 1592, the throne of Sweden went to his nephew and Habsburg ally, Sigismund of Poland and Sweden. During the tense political times which prevailed, Charles viewed the inheritance of the throne of Protestant Sweden by his devout Roman Catholic nephew with alarm. Thus, several years of religious controversy and discord followed.

During the period, he and the Swedish privy council ruled in Sigismund's name while he stayed in Poland. After various preliminaries, the Riksens ständer forced Sigismund to abdicate the throne to Charles IX in 1595. This eventually kicked off nearly seven decades of sporadic warfare as the two lines of the divided House of Vasa both continued to attempt to remake the union between the Polish and Swedish thrones with opposing counter-claims and dynastic wars.

Quite likely, the dynastic outcome between Sweden and Poland's house of Vasa exacerbated and radicalized the later actions of Europe's Catholic princes in the German states such as the Edict of Restitution. In fact, it worsened European politics to the abandonment or prevention of settling events by diplomacy and compromise during the vast bloodletting that was the Thirty Years' war.